ISING MODEL SIMULATIONS AS A TESTBED OF NUCLEATION THEORY

In this short review article we discuss the use of Ising lattice model as a testbed for improvement of theory of both homogeneous and heterogeneous nucleation theory. First we briefly overview the classical nucleation theory (CNT), and two typical simple systems on which simulations are performed - hard spheres, and Ising lattice model. Than we overview some results obtained by this approach and point to possible new directions of research and improvement

Nukleace v komplexních systémech

Název: Nukleace v komplexních systémech Autor: Jan Kulveit Pracoviště: Fyzikální ústav AV ČR, v. v. i. Vedoucí práce: prof. Pavel Demo, Fyzikální ústav AV ČR, v. v. i., Oddělění optických materiálů Abstrakt: V této práci studujeme nukleaci v postupně abstraktnějších kon- textech a systémech, počínaje klasickou teorií nukleace a konče nukleací v kom- plexních sítích. Mezi studované případy patří nukleace nečistot v pevné matrici na několika krystalech alkalických halogenidů, kde jsme stanovili formační en- ergie pro klastry, počínaje jednoduchým dipólem bez nečistot a malými agregáty až po možné konfigurace větších shluků. V další části se zaměříme na studium heterogenní nukleace. Zatímco v obvyklých modelech heterogenní nukleace se předpokládá, že povrchová energie je homogenní, ptáme se, co se stane, pokud budeme považovat povrchovou energii za heterogenní. S pomocí umbrella sam- pling zjišťujeme, že nukleační bariéra může být výrazně snížena v případě že povrch je heterogenní, i když je průměrná povrchová energie konstantní. V poslední části studujeme vliv koeficientu clusterování na fázové přechody v kom- plexních sítích pomocí FFS. Klíčová slova: nukleace, komplexní systémy,...Title: Nucleation in complex systems Author: Jan Kulveit Institute: Institute of Physics of the Czech Academy of Sciences Supervisor: prof. Pavel Demo, Institute of Physics of the Czech Academy ofSciences, Department of Optical Materials Abstract: We studied nucleation in progressively more abstract contexts and systems, starting from classical nucleation theory and ending with nucleation in complex networks. The cases studied include impurity nucleation in a solid matrix on several alkali halide crystals, where we determined formation energies for clusters, treated as defects, starting from single impurity-vacancy dipole and small aggregates to possible configurations of larger clusters. In the next part, we turn to the study of heterogeneous nucleation. While in the usual treatment of heterogeneous nucleation the surface energy is assumed to be homogenous, we ask the question what happens if we consider the surface energy to be heteroge- neous.Utilizing umbrella sampling computer simulations we find the nucleation barrier can be significantly lowered in the presence of surface heterogeneity, even if the average surface energy is kept constant. In the last part we study influence of clustering coefficient on phase transitions in scale-free networks, using forward flux sampling (FFS). Keywords: nucleation,...Matematicko-fyzikální fakultaFaculty of Mathematics and Physic

Studium nukleace kvantových teček

Kvantové tečky jsou předmětem rostoucího zájmu v mnoha vědeckých oborech. Kromě jiných metod mohou kvantové tečky vznikat také nukleací. V předložené práci studujeme počáteční stádium nukleace v krystalech NaCl a KCl počítačovým modelováním krystalové mříže. V systému NaCl-Pb mají nejstabilnější malé klastry rovinnou strukturu v {1; 1; 1}Na rovině okolní mříže a nukleuje přechodná 2D fáze. Oproti tomu v KCl-Pb jsou nejstabilnější klastry se strukturou Suzukiho fáze a nukleuje Suzukiho fáze. Vytvoření této fáze znesnadňuje další přechod ke stabilní PbCl2 struktuře. Tyto výsledky počítačového modelování jsou ve shodě s experimentálně pozorovanými rozdíly v chování KCl-Pb a NaCl-Pb.Quantum dots are increasingly important in many fields of science. Aminy other methods, quantum dots can also be formed by nucleation processes. In present work we study early stage of nucleation in NaCl and KCl crystals doped with PbCl2. Defect energies of small Pb clusters were calculated using numerical lattice methods. In NaCl-Pb system most stable small clusters have planar structure in {1; 1; 1}Na host lattice plane and intermittent planar phase nucleates. In contrast in KCl-Pb system small clusters with Suzuki phase structure are most stable and Suzuki phase nucleates. Formation of Suzuki phase hinders further transition to stable structure. These results of computer simulation are in agreemend with experimentally observed differences in KCl-Pb and NaCl-Pb systems behavior.Institute of Theoretical PhysicsÚstav teoretické fyzikyFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Predictive Minds: LLMs As Atypical Active Inference Agents

Large language models (LLMs) like GPT are often conceptualized as passive predictors, simulators, or even stochastic parrots. We instead conceptualize LLMs by drawing on the theory of active inference originating in cognitive science and neuroscience. We examine similarities and differences between traditional active inference systems and LLMs, leading to the conclusion that, currently, LLMs lack a tight feedback loop between acting in the world and perceiving the impacts of their actions, but otherwise fit in the active inference paradigm. We list reasons why this loop may soon be closed, and possible consequences of this including enhanced model self-awareness and the drive to minimize prediction error by changing the world.Comment: 6 page

Seasonal variation in SARS-CoV-2 transmission in temperate climates: a Bayesian modelling study in 143 European regions

Although seasonal variation has a known influence on the transmission of several respiratory viral infections, its role in SARS-CoV-2 transmission remains unclear. While there is a sizable and growing literature on environmental drivers of COVID-19 transmission, recent reviews have highlighted conflicting and inconclusive findings. This indeterminacy partly owes to the fact that seasonal variation relates to viral transmission by a complicated web of causal pathways, including many interacting biological and behavioural factors. Since analyses of specific factors cannot determine the aggregate strength of seasonal forcing, we sidestep the challenge of disentangling various possible causal paths in favor of a holistic approach. We model seasonality as a sinusoidal variation in transmission and infer a single Bayesian estimate of the overall seasonal effect. By extending two state-of-the-art models of non-pharmaceutical intervention (NPI) effects and their datasets covering 143 regions in temperate Europe, we are able to adjust our estimates for the role of both NPIs and mobility patterns in reducing transmission. We find strong seasonal patterns, consistent with a reduction in the time-varying reproduction number R(t) (the expected number of new infections generated by an infectious individual at time t) of 42.1% (95% CI: 24.7%—53.4%) from the peak of winter to the peak of summer. These results imply that the seasonality of SARSCoV-2 transmission is comparable in magnitude to the most effective individual NPIs but less than the combined effect of multiple interventions

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe.

Funder: European and Developing Countries Clinical Trials Partnership (EDCTP); doi: https://doi.org/10.13039/501100001713Funder: MRC Centre for Global Infectious Disease Analysis (MR/R015600/1), jointly funded by the U.K. Medical Research Council (MRC) and the U.K. Foreign, Commonwealth and Development Office (FCDO), under the MRC/FCDO Concordat agreement. Community Jameel. The UK Research and Innovation (MR/V038109/1), the Academy of Medical Sciences Springboard Award (SBF004/1080), The MRC (MR/R015600/1), The BMGF (OPP1197730), Imperial College Healthcare NHS Trust- BRC Funding (RDA02), The Novo Nordisk Young Investigator Award (NNF20OC0059309) and The NIHR Health Protection Research Unit in Modelling Methodology. S. Bhatt thanks Microsoft AI for Health and Amazon AWS for computational credits.Funder: EA FundsFunder: University of Oxford (Oxford University); doi: https://doi.org/10.13039/501100000769Funder: DeepMindFunder: OpenPhilanthropyFunder: UKRI Centre for Doctoral Training in Interactive Artificial Intelligence (EP/S022937/1)Funder: Augustinus Fonden (Augustinus Foundation); doi: https://doi.org/10.13039/501100004954Funder: Knud Højgaards Fond (Knud Højgaard Fund); doi: https://doi.org/10.13039/501100009938Funder: Kai Lange og Gunhild Kai Langes Fond (Kai Lange and Gunhild Kai Lange Foundation); doi: https://doi.org/10.13039/501100008206Funder: Aage og Johanne Louis-Hansens Fond (Aage and Johanne Louis-Hansen Foundation); doi: https://doi.org/10.13039/501100010344Funder: William Demant FoundationFunder: Boehringer Ingelheim Fonds (Stiftung für medizinische Grundlagenforschung); doi: https://doi.org/10.13039/501100001645Funder: Imperial College COVID-19 Research FundFunder: Cancer Research UK (CRUK); doi: https://doi.org/10.13039/501100000289European governments use non-pharmaceutical interventions (NPIs) to control resurging waves of COVID-19. However, they only have outdated estimates for how effective individual NPIs were in the first wave. We estimate the effectiveness of 17 NPIs in Europe's second wave from subnational case and death data by introducing a flexible hierarchical Bayesian transmission model and collecting the largest dataset of NPI implementation dates across Europe. Business closures, educational institution closures, and gathering bans reduced transmission, but reduced it less than they did in the first wave. This difference is likely due to organisational safety measures and individual protective behaviours-such as distancing-which made various areas of public life safer and thereby reduced the effect of closing them. Specifically, we find smaller effects for closing educational institutions, suggesting that stringent safety measures made schools safer compared to the first wave. Second-wave estimates outperform previous estimates at predicting transmission in Europe's third wave

Nucleation of quantum dots

Quantum dots are increasingly important in many fields of science. Aminy other methods, quantum dots can also be formed by nucleation processes. In present work we study early stage of nucleation in NaCl and KCl crystals doped with PbCl2. Defect energies of small Pb clusters were calculated using numerical lattice methods. In NaCl-Pb system most stable small clusters have planar structure in {1; 1; 1}Na host lattice plane and intermittent planar phase nucleates. In contrast in KCl-Pb system small clusters with Suzuki phase structure are most stable and Suzuki phase nucleates. Formation of Suzuki phase hinders further transition to stable structure. These results of computer simulation are in agreemend with experimentally observed differences in KCl-Pb and NaCl-Pb systems behavior

Nucleation in complex systems

Title: Nucleation in complex systems Author: Jan Kulveit Institute: Institute of Physics of the Czech Academy of Sciences Supervisor: prof. Pavel Demo, Institute of Physics of the Czech Academy ofSciences, Department of Optical Materials Abstract: We studied nucleation in progressively more abstract contexts and systems, starting from classical nucleation theory and ending with nucleation in complex networks. The cases studied include impurity nucleation in a solid matrix on several alkali halide crystals, where we determined formation energies for clusters, treated as defects, starting from single impurity-vacancy dipole and small aggregates to possible configurations of larger clusters. In the next part, we turn to the study of heterogeneous nucleation. While in the usual treatment of heterogeneous nucleation the surface energy is assumed to be homogenous, we ask the question what happens if we consider the surface energy to be heteroge- neous.Utilizing umbrella sampling computer simulations we find the nucleation barrier can be significantly lowered in the presence of surface heterogeneity, even if the average surface energy is kept constant. In the last part we study influence of clustering coefficient on phase transitions in scale-free networks, using forward flux sampling (FFS). Keywords: nucleation,..